On November 26, your press counsellor sent a letter to the Guardian taking strong exception to a sentence in my column of the same day. The sentence read: "In Iraq, US forces and their Iraqi surrogates are no longer bothering to conceal attacks on civilian targets and are openly eliminating anyone - doctors, clerics, journalists - who dares to count the bodies." Of particular concern was the word "eliminating".

The letter suggested that my charge was "baseless" and asked the Guardian either to withdraw it, or provide "evidence of this extremely grave accusation". It is quite rare for US embassy officials to openly involve themselves in the free press of a foreign country, so I took the letter extremely seriously. But while I agree that the accusation is grave, I have no intention of withdrawing it. Here, instead, is the evidence you requested.

In April, US forces laid siege to Falluja in retaliation for the gruesome killings of four Blackwater employees. The operation was a failure, with US troops eventually handing the city back to resistance forces. The reason for the withdrawal was that the siege had sparked uprisings across the country, triggered by reports that hundreds of civilians had been killed. This information came from three main sources:

1) Doctors. USA Today reported on April 11 that "Statistics and names of the dead were gathered from four main clinics around the city and from Falluja general hospital".

2) Arab TV journalists. While doctors reported the numbers of dead, it was al-Jazeera and al-Arabiya that put a human face on those statistics. With unembedded camera crews in Falluja, both networks beamed footage of mutilated women and children throughout Iraq and the Arab-speaking world.

3) Clerics. The reports of high civilian casualties coming from journalists and doctors were seized upon by prominent clerics in Iraq. Many delivered fiery sermons condemning the attack, turning their congregants against US forces and igniting the uprising that forced US troops to withdraw.

US authorities have denied that hundreds of civilians were killed during last April's siege, and have lashed out at the sources of these reports. For instance, an unnamed "senior American officer", speaking to the New York Times last month, labelled Falluja general hospital "a centre of propaganda". But the strongest words were reserved for Arab TV networks. When asked about al-Jazeera and al-Arabiya's reports that hundreds of civilians had been killed in Falluja, Donald Rumsfeld, the US secretary of defence, replied that "what al-Jazeera is doing is vicious, inaccurate and inexcusable ... " Last month, US troops once again laid siege to Falluja - but this time the attack included a new tactic: eliminating the doctors, journalists and clerics who focused public attention on civilian casualties last time around.

Eliminating doctors

The first major operation by US marines and Iraqi soldiers was to storm Falluja general hospital, arresting doctors and placing the facility under military control. The New York Times reported that "the hospital was selected as an early target because the American military believed that it was the source of rumours about heavy casual ties", noting that "this time around, the American military intends to fight its own information war, countering or squelching what has been one of the insurgents' most potent weapons". The Los Angeles Times quoted a doctor as saying that the soldiers "stole the mobile phones" at the hospital - preventing doctors from communicating with the outside world.

But this was not the worst of the attacks on health workers. Two days earlier, a crucial emergency health clinic was bombed to rubble, as well as a medical supplies dispensary next door. Dr Sami al-Jumaili, who was working in the clinic, says the bombs took the lives of 15 medics, four nurses and 35 patients. The Los Angeles Times reported that the manager of Falluja general hospital "had told a US general the location of the downtown makeshift medical centre" before it was hit.

Whether the clinic was targeted or destroyed accidentally, the effect was the same: to eliminate many of Falluja's doctors from the war zone. As Dr Jumaili told the Independent on November 14: "There is not a single surgeon in Falluja." When fighting moved to Mosul, a similar tactic was used: on entering the city, US and Iraqi forces immediately seized control of the al-Zaharawi hospital.

Eliminating journalists

The images from last month's siege on Falluja came almost exclusively from reporters embedded with US troops. This is because Arab journalists who had covered April's siege from the civilian perspective had effectively been eliminated. Al-Jazeera had no cameras on the ground because it has been banned from reporting in Iraq indefinitely. Al-Arabiya did have an unembedded reporter, Abdel Kader Al-Saadi, in Falluja, but on November 11 US forces arrested him and held him for the length of the siege. Al-Saadi's detention has been condemned by Reporters Without Borders and the International Federation of Journalists. "We cannot ignore the possibility that he is being intimidated for just trying to do his job," the IFJ stated.

It's not the first time journalists in Iraq have faced this kind of intimidation. When US forces invaded Baghdad in April 2003, US Central Command urged all unembedded journalists to leave the city. Some insisted on staying and at least three paid with their lives. On April 8, a US aircraft bombed al-Jazeera's Baghdad offices, killing reporter Tareq Ayyoub. Al-Jazeera has documentation proving it gave the coordinates of its location to US forces.

On the same day, a US tank fired on the Palestine hotel, killing José Couso, of the Spanish network Telecinco, and Taras Protsiuk, of Reuters. Three US soldiers are facing a criminal lawsuit from Couso's family, which alleges that US forces were well aware that journalists were in the Palestine hotel and that they committed a war crime.

Eliminating clerics

Just as doctors and journalists have been targeted, so too have many of the clerics who have spoken out forcefully against the killings in Falluja. On November 11, Sheik Mahdi al-Sumaidaei, the head of the Supreme Association for Guidance and Daawa, was arrested. According to Associated Press, "Al-Sumaidaei has called on the country's Sunni minority to launch a civil disobedience campaign if the Iraqi government does not halt the attack on Falluja". On November 19, AP reported that US and Iraqi forces stormed a prominent Sunni mosque, the Abu Hanifa, in Aadhamiya, killing three people and arresting 40, including the chief cleric - another opponent of the Falluja siege. On the same day, Fox News reported that "US troops also raided a Sunni mosque in Qaim, near the Syrian border". The report described the arrests as "retaliation for opposing the Falluja offensive". Two Shia clerics associated with Moqtada al-Sadr have also been arrested in recent weeks; according to AP, "both had spoken out against the Falluja attack".

"We don't do body counts," said General Tommy Franks of US Central Command. The question is: what happens to the people who insist on counting the bodies - the doctors who must pronounce their patients dead, the journalists who document these losses, the clerics who denounce them? In Iraq, evidence is mounting that these voices are being systematically silenced through a variety of means, from mass arrests, to raids on hospitals, media bans, and overt and unexplained physical attacks.

Mr Ambassador, I believe that your government and its Iraqi surrogates are waging two wars in Iraq. One war is against the Iraqi people, and it has claimed an estimated 100,000 lives. The other is a war on witnesses.